User:Steven Tuyishime - Revision history

Steven Tuyishime at 20:02, 21 December 2008

Steven Tuyishime — Sun, 21 Dec 2008 20:02:37 GMT

←Older revision		Revision as of 20:02, 21 December 2008
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	For more information on CATH and the different classifications that are defined, consult the article by Orengo et al<ref>		For more information on CATH and the different classifications that are defined, consult the article by Orengo et al<ref>
	C. A. Orengo, A. D. Michie, S. Jones, D. T. Jones, M. B. Swindells, and J. M. Thornton. CATH–a		C. A. Orengo, A. D. Michie, S. Jones, D. T. Jones, M. B. Swindells, and J. M. Thornton. CATH–a
-	hierarchic classification of protein domain structures. Structure, 5(8):1093–1108, Aug 1997.</ref> or visit the cath website at http://www.cathdb.info/~~cathnode~~	+	hierarchic classification of protein domain structures. Structure, 5(8):1093–1108, Aug 1997.</ref> or visit the cath website at http://www.cathdb.info/

Steven Tuyishime at 01:44, 20 December 2008

Steven Tuyishime — Sat, 20 Dec 2008 01:44:16 GMT

←Older revision		Revision as of 01:44, 20 December 2008
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	Looking at Glutamine Synthetase in ''Salmonella typhimurium'', we can identify <scene name='User:Steven_Tuyishime/2_cath_domains/1'>2 CATH domains</scene>, with the smaller domain encompassing residues 1-103 (in red) and the other residues 104-456 (in blue). Each of the domains are of the class Alpha Beta, however, that is the only common aspect between the two. Alpha Beta includes both alternating alpha/beta structures and alpha+beta structures. <scene name='User:Steven_Tuyishime/Domain_from_104_to_456/2'>One domain begins at residue 104 and goes to residue 456</scene>. For this domain, the Architecture is a <scene name='User:Steven_Tuyishime/2_layer_sandwich/4'>2 layer sandwich</scene>, another example of a 2 layer sandwich can be found at http://www.cathdb.info/cathnode/3.30. A 2 layer sandwich consists of a layer of alpha helices and a layer of beta sheets forming a sandwich like structure. The Topology is Creatine Kinase; Chain A, domain 2 and the Homologous superfamily is Creatine Kinase; Chain. This domain is the larger of the two and has a COOH terminus.		Looking at Glutamine Synthetase in ''Salmonella typhimurium'', we can identify <scene name='User:Steven_Tuyishime/2_cath_domains/1'>2 CATH domains</scene>, with the smaller domain encompassing residues 1-103 (in red) and the other residues 104-456 (in blue). Each of the domains are of the class Alpha Beta, however, that is the only common aspect between the two. Alpha Beta includes both alternating alpha/beta structures and alpha+beta structures. <scene name='User:Steven_Tuyishime/Domain_from_104_to_456/2'>One domain begins at residue 104 and goes to residue 456</scene>. For this domain, the Architecture is a <scene name='User:Steven_Tuyishime/2_layer_sandwich/4'>2 layer sandwich</scene>, another example of a 2 layer sandwich can be found at http://www.cathdb.info/cathnode/3.30. A 2 layer sandwich consists of a layer of alpha helices and a layer of beta sheets forming a sandwich like structure. The Topology is Creatine Kinase; Chain A, domain 2 and the Homologous superfamily is Creatine Kinase; Chain. This domain is the larger of the two and has a COOH terminus.

-	<scene name='User:Steven_Tuyishime/Domain_from_1_to_103/3'>The second domain in S. typhimurium begins at residue 1 and goes to residue 103</scene>. In this domain, the architecture is a roll because the alpha helices and beta sheets form a roll-like structure. The topology is <scene name='User:Steven_Tuyishime/Ubiquitin_like_roll/7'>ubiquitin-like, or a UB-roll</scene> and the Homologous superfamily has no defined name. This domain is smaller and has an NH2 terminus. It is covalently linked to the larger COOH terminus(the first domain described in prior paragraph). This NH2 terminus is exposed compared to the buried COOH terminus of the larger domain <ref> Yamashita MM, Almassy RJ, Janson CA, Cascio D, Eisenberg . 1989. JBiol Chem 264:17681-17690. Refined atomic model of glutamine synthetase at 3.5 A resolution.</ref>.	+	<scene name='User:Steven_Tuyishime/Domain_from_1_to_103/3'>The second domain in S. typhimurium begins at residue 1 and goes to residue 103</scene>. In this domain, the architecture is a roll because the alpha helices and beta sheets form a roll-like structure. The topology is <scene name='User:Steven_Tuyishime/Ubiquitin_like_roll/7'>ubiquitin-like, or a UB-roll</scene> due to its resemblance to a cartoon depiction of ubiquitin <ref> http://en.wikipedia.org/wiki/Ubiquitin</ref> and the Homologous superfamily has no defined name. This domain is smaller and has an NH2 terminus. It is covalently linked to the larger COOH terminus(the first domain described in prior paragraph). This NH2 terminus is exposed compared to the buried COOH terminus of the larger domain <ref> Yamashita MM, Almassy RJ, Janson CA, Cascio D, Eisenberg . 1989. JBiol Chem 264:17681-17690. Refined atomic model of glutamine synthetase at 3.5 A resolution.</ref>.

	For more information on CATH and the different classifications that are defined, consult the article by Orengo et al<ref>		For more information on CATH and the different classifications that are defined, consult the article by Orengo et al<ref>

Steven Tuyishime at 23:29, 19 December 2008

Steven Tuyishime — Fri, 19 Dec 2008 23:29:11 GMT

←Older revision		Revision as of 23:29, 19 December 2008
Line 13:		Line 13:
	For more information on CATH and the different classifications that are defined, consult the article by Orengo et al<ref>		For more information on CATH and the different classifications that are defined, consult the article by Orengo et al<ref>
	C. A. Orengo, A. D. Michie, S. Jones, D. T. Jones, M. B. Swindells, and J. M. Thornton. CATH–a		C. A. Orengo, A. D. Michie, S. Jones, D. T. Jones, M. B. Swindells, and J. M. Thornton. CATH–a
-	hierarchic classification of protein domain structures. Structure, 5(8):1093–1108, Aug 1997.</ref>	+	hierarchic classification of protein domain structures. Structure, 5(8):1093–1108, Aug 1997.</ref> or visit the cath website at http://www.cathdb.info/cathnode

Steven Tuyishime at 23:25, 19 December 2008

Steven Tuyishime — Fri, 19 Dec 2008 23:25:22 GMT

←Older revision		Revision as of 23:25, 19 December 2008
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	Looking at Glutamine Synthetase in ''Salmonella typhimurium'', we can identify <scene name='User:Steven_Tuyishime/2_cath_domains/1'>2 CATH domains</scene>, with the smaller domain encompassing residues 1-103 (in red) and the other residues 104-456 (in blue). Each of the domains are of the class Alpha Beta, however, that is the only common aspect between the two. Alpha Beta includes both alternating alpha/beta structures and alpha+beta structures. <scene name='User:Steven_Tuyishime/Domain_from_104_to_456/2'>One domain begins at residue 104 and goes to residue 456</scene>. For this domain, the Architecture is a <scene name='User:Steven_Tuyishime/2_layer_sandwich/4'>2 layer sandwich</scene>, another example of a 2 layer sandwich can be found at http://www.cathdb.info/cathnode/3.30. A 2 layer sandwich consists of a layer of alpha helices and a layer of beta sheets forming a sandwich like structure. The Topology is Creatine Kinase; Chain A, domain 2 and the Homologous superfamily is Creatine Kinase; Chain. This domain is the larger of the two and has a COOH terminus.		Looking at Glutamine Synthetase in ''Salmonella typhimurium'', we can identify <scene name='User:Steven_Tuyishime/2_cath_domains/1'>2 CATH domains</scene>, with the smaller domain encompassing residues 1-103 (in red) and the other residues 104-456 (in blue). Each of the domains are of the class Alpha Beta, however, that is the only common aspect between the two. Alpha Beta includes both alternating alpha/beta structures and alpha+beta structures. <scene name='User:Steven_Tuyishime/Domain_from_104_to_456/2'>One domain begins at residue 104 and goes to residue 456</scene>. For this domain, the Architecture is a <scene name='User:Steven_Tuyishime/2_layer_sandwich/4'>2 layer sandwich</scene>, another example of a 2 layer sandwich can be found at http://www.cathdb.info/cathnode/3.30. A 2 layer sandwich consists of a layer of alpha helices and a layer of beta sheets forming a sandwich like structure. The Topology is Creatine Kinase; Chain A, domain 2 and the Homologous superfamily is Creatine Kinase; Chain. This domain is the larger of the two and has a COOH terminus.

-	<scene name='User:Steven_Tuyishime/Domain_from_1_to_103/3'>The second domain in S. typhimurium begins at residue 1 and goes to residue 103</scene>. In this domain, the architecture is a roll. The topology is <scene name='User:Steven_Tuyishime/Ubiquitin_like_roll/7'>ubiquitin-like, or a UB-roll</scene> and the Homologous superfamily has no defined name. This domain is smaller and has an NH2 terminus. It is covalently linked to the larger COOH terminus(the first domain described in prior paragraph). This NH2 terminus is exposed compared to the buried COOH terminus of the larger domain <ref> Yamashita MM, Almassy RJ, Janson CA, Cascio D, Eisenberg . 1989. JBiol Chem 264:17681-17690. Refined atomic model of glutamine synthetase at 3.5 A resolution.</ref>.	+	<scene name='User:Steven_Tuyishime/Domain_from_1_to_103/3'>The second domain in S. typhimurium begins at residue 1 and goes to residue 103</scene>. In this domain, the architecture is a roll because the alpha helices and beta sheets form a roll-like structure. The topology is <scene name='User:Steven_Tuyishime/Ubiquitin_like_roll/7'>ubiquitin-like, or a UB-roll</scene> and the Homologous superfamily has no defined name. This domain is smaller and has an NH2 terminus. It is covalently linked to the larger COOH terminus(the first domain described in prior paragraph). This NH2 terminus is exposed compared to the buried COOH terminus of the larger domain <ref> Yamashita MM, Almassy RJ, Janson CA, Cascio D, Eisenberg . 1989. JBiol Chem 264:17681-17690. Refined atomic model of glutamine synthetase at 3.5 A resolution.</ref>.

		+	For more information on CATH and the different classifications that are defined, consult the article by Orengo et al<ref>
		+	C. A. Orengo, A. D. Michie, S. Jones, D. T. Jones, M. B. Swindells, and J. M. Thornton. CATH–a
		+	hierarchic classification of protein domain structures. Structure, 5(8):1093–1108, Aug 1997.</ref>

Steven Tuyishime at 23:13, 19 December 2008

Steven Tuyishime — Fri, 19 Dec 2008 23:13:50 GMT

←Older revision		Revision as of 23:13, 19 December 2008
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	Looking at Glutamine Synthetase in ''Salmonella typhimurium'', we can identify <scene name='User:Steven_Tuyishime/2_cath_domains/1'>2 CATH domains</scene>, with the smaller domain encompassing residues 1-103 (in red) and the other residues 104-456 (in blue). Each of the domains are of the class Alpha Beta, however, that is the only common aspect between the two. Alpha Beta includes both alternating alpha/beta structures and alpha+beta structures. <scene name='User:Steven_Tuyishime/Domain_from_104_to_456/2'>One domain begins at residue 104 and goes to residue 456</scene>. For this domain, the Architecture is a <scene name='User:Steven_Tuyishime/2_layer_sandwich/4'>2 layer sandwich</scene>, another example of a 2 layer sandwich can be found at http://www.cathdb.info/cathnode/3.30. A 2 layer sandwich consists of a layer of alpha helices and a layer of beta sheets forming a sandwich like structure. The Topology is Creatine Kinase; Chain A, domain 2 and the Homologous superfamily is Creatine Kinase; Chain. This domain is the larger of the two and has a COOH terminus.		Looking at Glutamine Synthetase in ''Salmonella typhimurium'', we can identify <scene name='User:Steven_Tuyishime/2_cath_domains/1'>2 CATH domains</scene>, with the smaller domain encompassing residues 1-103 (in red) and the other residues 104-456 (in blue). Each of the domains are of the class Alpha Beta, however, that is the only common aspect between the two. Alpha Beta includes both alternating alpha/beta structures and alpha+beta structures. <scene name='User:Steven_Tuyishime/Domain_from_104_to_456/2'>One domain begins at residue 104 and goes to residue 456</scene>. For this domain, the Architecture is a <scene name='User:Steven_Tuyishime/2_layer_sandwich/4'>2 layer sandwich</scene>, another example of a 2 layer sandwich can be found at http://www.cathdb.info/cathnode/3.30. A 2 layer sandwich consists of a layer of alpha helices and a layer of beta sheets forming a sandwich like structure. The Topology is Creatine Kinase; Chain A, domain 2 and the Homologous superfamily is Creatine Kinase; Chain. This domain is the larger of the two and has a COOH terminus.

-	<scene name='User:Steven_Tuyishime/Domain_from_1_to_103/3'>The second domain in S. typhimurium begins at residue 1 and goes to residue 103</scene>. In this domain, the architecture is a roll. The topology is <scene name='User:Steven_Tuyishime/Ubiquitin_like_roll/3'>ubiquitin-like, or a UB-roll</scene> and the Homologous superfamily has no defined name. This domain is smaller and has an NH2 terminus. It is covalently linked to the larger COOH terminus(the first domain described in prior paragraph). This NH2 terminus is exposed compared to the buried COOH terminus of the larger domain <ref> Yamashita MM, Almassy RJ, Janson CA, Cascio D, Eisenberg . 1989. JBiol Chem 264:17681-17690. Refined atomic model of glutamine synthetase at 3.5 A resolution.</ref>.	+	<scene name='User:Steven_Tuyishime/Domain_from_1_to_103/3'>The second domain in S. typhimurium begins at residue 1 and goes to residue 103</scene>. In this domain, the architecture is a roll. The topology is <scene name='User:Steven_Tuyishime/Ubiquitin_like_roll/7'>ubiquitin-like, or a UB-roll</scene> and the Homologous superfamily has no defined name. This domain is smaller and has an NH2 terminus. It is covalently linked to the larger COOH terminus(the first domain described in prior paragraph). This NH2 terminus is exposed compared to the buried COOH terminus of the larger domain <ref> Yamashita MM, Almassy RJ, Janson CA, Cascio D, Eisenberg . 1989. JBiol Chem 264:17681-17690. Refined atomic model of glutamine synthetase at 3.5 A resolution.</ref>.

Steven Tuyishime at 23:06, 19 December 2008

Steven Tuyishime — Fri, 19 Dec 2008 23:06:35 GMT

←Older revision		Revision as of 23:06, 19 December 2008
Line 9:		Line 9:
	Looking at Glutamine Synthetase in ''Salmonella typhimurium'', we can identify <scene name='User:Steven_Tuyishime/2_cath_domains/1'>2 CATH domains</scene>, with the smaller domain encompassing residues 1-103 (in red) and the other residues 104-456 (in blue). Each of the domains are of the class Alpha Beta, however, that is the only common aspect between the two. Alpha Beta includes both alternating alpha/beta structures and alpha+beta structures. <scene name='User:Steven_Tuyishime/Domain_from_104_to_456/2'>One domain begins at residue 104 and goes to residue 456</scene>. For this domain, the Architecture is a <scene name='User:Steven_Tuyishime/2_layer_sandwich/4'>2 layer sandwich</scene>, another example of a 2 layer sandwich can be found at http://www.cathdb.info/cathnode/3.30. A 2 layer sandwich consists of a layer of alpha helices and a layer of beta sheets forming a sandwich like structure. The Topology is Creatine Kinase; Chain A, domain 2 and the Homologous superfamily is Creatine Kinase; Chain. This domain is the larger of the two and has a COOH terminus.		Looking at Glutamine Synthetase in ''Salmonella typhimurium'', we can identify <scene name='User:Steven_Tuyishime/2_cath_domains/1'>2 CATH domains</scene>, with the smaller domain encompassing residues 1-103 (in red) and the other residues 104-456 (in blue). Each of the domains are of the class Alpha Beta, however, that is the only common aspect between the two. Alpha Beta includes both alternating alpha/beta structures and alpha+beta structures. <scene name='User:Steven_Tuyishime/Domain_from_104_to_456/2'>One domain begins at residue 104 and goes to residue 456</scene>. For this domain, the Architecture is a <scene name='User:Steven_Tuyishime/2_layer_sandwich/4'>2 layer sandwich</scene>, another example of a 2 layer sandwich can be found at http://www.cathdb.info/cathnode/3.30. A 2 layer sandwich consists of a layer of alpha helices and a layer of beta sheets forming a sandwich like structure. The Topology is Creatine Kinase; Chain A, domain 2 and the Homologous superfamily is Creatine Kinase; Chain. This domain is the larger of the two and has a COOH terminus.

-	<scene name='User:Steven_Tuyishime/Domain_from_1_to_103/3'>The second domain in S. typhimurium begins at residue 1 and goes to residue 103</scene>. In this domain, the architecture is a roll. The topology is <scene name='User:Steven_Tuyishime/Ubiquitin_like_roll/2'>ubiquitin-like, or a UB-roll</scene> and the Homologous superfamily has no defined name. This domain is smaller and has an NH2 terminus.	+	<scene name='User:Steven_Tuyishime/Domain_from_1_to_103/3'>The second domain in S. typhimurium begins at residue 1 and goes to residue 103</scene>. In this domain, the architecture is a roll. The topology is <scene name='User:Steven_Tuyishime/Ubiquitin_like_roll/3'>ubiquitin-like, or a UB-roll</scene> and the Homologous superfamily has no defined name. This domain is smaller and has an NH2 terminus. It is covalently linked to the larger COOH terminus(the first domain described in prior paragraph). This NH2 terminus is exposed compared to the buried COOH terminus of the larger domain <ref> Yamashita MM, Almassy RJ, Janson CA, Cascio D, Eisenberg . 1989. JBiol Chem 264:17681-17690. Refined atomic model of glutamine synthetase at 3.5 A resolution.</ref>.
-	It is covalently linked to the larger COOH terminus(the first domain described in prior paragraph). This NH2 terminus is exposed compared to the buried COOH terminus of the larger domain <ref> Yamashita MM, Almassy RJ, Janson CA, Cascio D, ~~EisenberDg~~ . 1989. JBiol Chem 264:17681-17690. Refined atomic model of glutamine synthetase at 3.5 A resolution.</ref>.	+

Steven Tuyishime at 22:55, 19 December 2008

Steven Tuyishime — Fri, 19 Dec 2008 22:55:37 GMT

←Older revision		Revision as of 22:55, 19 December 2008
Line 9:		Line 9:
	Looking at Glutamine Synthetase in ''Salmonella typhimurium'', we can identify <scene name='User:Steven_Tuyishime/2_cath_domains/1'>2 CATH domains</scene>, with the smaller domain encompassing residues 1-103 (in red) and the other residues 104-456 (in blue). Each of the domains are of the class Alpha Beta, however, that is the only common aspect between the two. Alpha Beta includes both alternating alpha/beta structures and alpha+beta structures. <scene name='User:Steven_Tuyishime/Domain_from_104_to_456/2'>One domain begins at residue 104 and goes to residue 456</scene>. For this domain, the Architecture is a <scene name='User:Steven_Tuyishime/2_layer_sandwich/4'>2 layer sandwich</scene>, another example of a 2 layer sandwich can be found at http://www.cathdb.info/cathnode/3.30. A 2 layer sandwich consists of a layer of alpha helices and a layer of beta sheets forming a sandwich like structure. The Topology is Creatine Kinase; Chain A, domain 2 and the Homologous superfamily is Creatine Kinase; Chain. This domain is the larger of the two and has a COOH terminus.		Looking at Glutamine Synthetase in ''Salmonella typhimurium'', we can identify <scene name='User:Steven_Tuyishime/2_cath_domains/1'>2 CATH domains</scene>, with the smaller domain encompassing residues 1-103 (in red) and the other residues 104-456 (in blue). Each of the domains are of the class Alpha Beta, however, that is the only common aspect between the two. Alpha Beta includes both alternating alpha/beta structures and alpha+beta structures. <scene name='User:Steven_Tuyishime/Domain_from_104_to_456/2'>One domain begins at residue 104 and goes to residue 456</scene>. For this domain, the Architecture is a <scene name='User:Steven_Tuyishime/2_layer_sandwich/4'>2 layer sandwich</scene>, another example of a 2 layer sandwich can be found at http://www.cathdb.info/cathnode/3.30. A 2 layer sandwich consists of a layer of alpha helices and a layer of beta sheets forming a sandwich like structure. The Topology is Creatine Kinase; Chain A, domain 2 and the Homologous superfamily is Creatine Kinase; Chain. This domain is the larger of the two and has a COOH terminus.

-	<scene name='User:Steven_Tuyishime/Domain_from_1_to_103/1'>	+	<scene name='User:Steven_Tuyishime/Domain_from_1_to_103/3'>The second domain in S. typhimurium begins at residue 1 and goes to residue 103</scene>. In this domain, the architecture is a roll. The topology is <scene name='User:Steven_Tuyishime/Ubiquitin_like_roll/2'>ubiquitin-like, or a UB-roll</scene> and the Homologous superfamily has no defined name. This domain is smaller and has an NH2 terminus.
-	The second domain in S. typhimurium begins at residue 1 and goes to residue 103</scene>. In this domain, the architecture is a roll. The topology is <scene name='User:Steven_Tuyishime/Ubiquitin_like_roll/2'>ubiquitin-like, or a UB-roll</scene> and the Homologous superfamily has no defined name. This domain is smaller and has an NH2 terminus.	+
	It is covalently linked to the larger COOH terminus(the first domain described in prior paragraph). This NH2 terminus is exposed compared to the buried COOH terminus of the larger domain <ref> Yamashita MM, Almassy RJ, Janson CA, Cascio D, EisenberDg . 1989. JBiol Chem 264:17681-17690. Refined atomic model of glutamine synthetase at 3.5 A resolution.</ref>.		It is covalently linked to the larger COOH terminus(the first domain described in prior paragraph). This NH2 terminus is exposed compared to the buried COOH terminus of the larger domain <ref> Yamashita MM, Almassy RJ, Janson CA, Cascio D, EisenberDg . 1989. JBiol Chem 264:17681-17690. Refined atomic model of glutamine synthetase at 3.5 A resolution.</ref>.

Steven Tuyishime at 22:43, 19 December 2008

Steven Tuyishime — Fri, 19 Dec 2008 22:43:53 GMT

←Older revision		Revision as of 22:43, 19 December 2008
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	Glutamine Synthetase (GS) has 2 prominent CATH domains. CATH is an acronym for Class (C), Architecture (A), Topology (T), and Homologous superfamily (H), which are categories for protein classification. Each of the aforementioned levels are used to classify molecules in a hierarchical manner. The highest order classification of a molecule is Class. A molecule can be classified by any one of 4 classes: Mainly Alpha, Mainly Beta, Alpha Beta, and Few Secondary Structures <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>. Another level of classification which is on a lower order than class is Architecture. This level of classification is used to identify the shape of the domain structure using the orientation of secondary structures but ignoring the way they are connected to each other <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>. A third level of classification is Topology, which is also called Fold Group. This classification concerns the shared similarity of overall shape and connectivity of the secondary structures in the domain core <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>. The Homologous superfamily refers to a fourth classification type. This hierarchy groups together protein domains which are thought to share a common ancestor, according to specific criteria <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>.		Glutamine Synthetase (GS) has 2 prominent CATH domains. CATH is an acronym for Class (C), Architecture (A), Topology (T), and Homologous superfamily (H), which are categories for protein classification. Each of the aforementioned levels are used to classify molecules in a hierarchical manner. The highest order classification of a molecule is Class. A molecule can be classified by any one of 4 classes: Mainly Alpha, Mainly Beta, Alpha Beta, and Few Secondary Structures <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>. Another level of classification which is on a lower order than class is Architecture. This level of classification is used to identify the shape of the domain structure using the orientation of secondary structures but ignoring the way they are connected to each other <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>. A third level of classification is Topology, which is also called Fold Group. This classification concerns the shared similarity of overall shape and connectivity of the secondary structures in the domain core <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>. The Homologous superfamily refers to a fourth classification type. This hierarchy groups together protein domains which are thought to share a common ancestor, according to specific criteria <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>.

-	Looking at Glutamine Synthetase in ''Salmonella typhimurium'', we can identify <scene name='User:Steven_Tuyishime/2_cath_domains/1'>2 CATH domains</scene>, with the smaller domain encompassing residues 1-103 (in red) and the other residues 104-456 (in blue). Each of the domains are of the class Alpha Beta, however, that is the only common aspect between the two. Alpha Beta includes both alternating alpha/beta structures and alpha+beta structures. <scene name='User:Steven_Tuyishime/Domain_from_104_to_456/1'>One domain begins at residue 104 and goes to residue 456</scene>. For this domain, the Architecture is a <scene name='User:Steven_Tuyishime/2_layer_sandwich/4'>2 layer sandwich</scene>, another example of a 2 layer sandwich can be found at http://www.cathdb.info/cathnode/3.30. A 2 layer sandwich consists of a layer of alpha helices and a layer of beta sheets forming a sandwich like structure. The Topology is Creatine Kinase; Chain A, domain 2 and the Homologous superfamily is Creatine Kinase; Chain. This domain is the larger of the two and has a COOH terminus.	+	Looking at Glutamine Synthetase in ''Salmonella typhimurium'', we can identify <scene name='User:Steven_Tuyishime/2_cath_domains/1'>2 CATH domains</scene>, with the smaller domain encompassing residues 1-103 (in red) and the other residues 104-456 (in blue). Each of the domains are of the class Alpha Beta, however, that is the only common aspect between the two. Alpha Beta includes both alternating alpha/beta structures and alpha+beta structures. <scene name='User:Steven_Tuyishime/Domain_from_104_to_456/2'>One domain begins at residue 104 and goes to residue 456</scene>. For this domain, the Architecture is a <scene name='User:Steven_Tuyishime/2_layer_sandwich/4'>2 layer sandwich</scene>, another example of a 2 layer sandwich can be found at http://www.cathdb.info/cathnode/3.30. A 2 layer sandwich consists of a layer of alpha helices and a layer of beta sheets forming a sandwich like structure. The Topology is Creatine Kinase; Chain A, domain 2 and the Homologous superfamily is Creatine Kinase; Chain. This domain is the larger of the two and has a COOH terminus.

	<scene name='User:Steven_Tuyishime/Domain_from_1_to_103/1'>		<scene name='User:Steven_Tuyishime/Domain_from_1_to_103/1'>

Steven Tuyishime at 22:38, 19 December 2008

Steven Tuyishime — Fri, 19 Dec 2008 22:38:05 GMT

←Older revision		Revision as of 22:38, 19 December 2008
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	Glutamine Synthetase (GS) has 2 prominent CATH domains. CATH is an acronym for Class (C), Architecture (A), Topology (T), and Homologous superfamily (H), which are categories for protein classification. Each of the aforementioned levels are used to classify molecules in a hierarchical manner. The highest order classification of a molecule is Class. A molecule can be classified by any one of 4 classes: Mainly Alpha, Mainly Beta, Alpha Beta, and Few Secondary Structures <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>. Another level of classification which is on a lower order than class is Architecture. This level of classification is used to identify the shape of the domain structure using the orientation of secondary structures but ignoring the way they are connected to each other <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>. A third level of classification is Topology, which is also called Fold Group. This classification concerns the shared similarity of overall shape and connectivity of the secondary structures in the domain core <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>. The Homologous superfamily refers to a fourth classification type. This hierarchy groups together protein domains which are thought to share a common ancestor, according to specific criteria <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>.		Glutamine Synthetase (GS) has 2 prominent CATH domains. CATH is an acronym for Class (C), Architecture (A), Topology (T), and Homologous superfamily (H), which are categories for protein classification. Each of the aforementioned levels are used to classify molecules in a hierarchical manner. The highest order classification of a molecule is Class. A molecule can be classified by any one of 4 classes: Mainly Alpha, Mainly Beta, Alpha Beta, and Few Secondary Structures <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>. Another level of classification which is on a lower order than class is Architecture. This level of classification is used to identify the shape of the domain structure using the orientation of secondary structures but ignoring the way they are connected to each other <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>. A third level of classification is Topology, which is also called Fold Group. This classification concerns the shared similarity of overall shape and connectivity of the secondary structures in the domain core <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>. The Homologous superfamily refers to a fourth classification type. This hierarchy groups together protein domains which are thought to share a common ancestor, according to specific criteria <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>.

-	Looking at Glutamine Synthetase in ''Salmonella typhimurium'', we can identify <scene name='User:Steven_Tuyishime/2_cath_domains/1'>2 CATH domains</scene>, with the smaller domain encompassing residues 1-103 (in red) and the other residues 104-456 (in blue). Each of the domains are of the class Alpha Beta, however, that is the only common aspect between the two. Alpha Beta includes both alternating alpha/beta structures and alpha+beta structures. <scene name='User:Steven_Tuyishime/Domain_from_104_to_456/1'>One domain begins at residue 104 and goes to residue 456</scene>. For this domain, the Architecture is a <scene name='User:Steven_Tuyishime/2_layer_sandwich/3'>2 layer sandwich</scene>. The Topology is Creatine Kinase; Chain A, domain 2 and the Homologous superfamily is Creatine Kinase; Chain. This domain is the larger of the two and has a COOH terminus.	+	Looking at Glutamine Synthetase in ''Salmonella typhimurium'', we can identify <scene name='User:Steven_Tuyishime/2_cath_domains/1'>2 CATH domains</scene>, with the smaller domain encompassing residues 1-103 (in red) and the other residues 104-456 (in blue). Each of the domains are of the class Alpha Beta, however, that is the only common aspect between the two. Alpha Beta includes both alternating alpha/beta structures and alpha+beta structures. <scene name='User:Steven_Tuyishime/Domain_from_104_to_456/1'>One domain begins at residue 104 and goes to residue 456</scene>. For this domain, the Architecture is a <scene name='User:Steven_Tuyishime/2_layer_sandwich/4'>2 layer sandwich</scene>, another example of a 2 layer sandwich can be found at http://www.cathdb.info/cathnode/3.30. A 2 layer sandwich consists of a layer of alpha helices and a layer of beta sheets forming a sandwich like structure. The Topology is Creatine Kinase; Chain A, domain 2 and the Homologous superfamily is Creatine Kinase; Chain. This domain is the larger of the two and has a COOH terminus.

	<scene name='User:Steven_Tuyishime/Domain_from_1_to_103/1'>		<scene name='User:Steven_Tuyishime/Domain_from_1_to_103/1'>

Steven Tuyishime at 22:16, 19 December 2008

Steven Tuyishime — Fri, 19 Dec 2008 22:16:06 GMT

←Older revision		Revision as of 22:16, 19 December 2008
Line 7:		Line 7:
	Glutamine Synthetase (GS) has 2 prominent CATH domains. CATH is an acronym for Class (C), Architecture (A), Topology (T), and Homologous superfamily (H), which are categories for protein classification. Each of the aforementioned levels are used to classify molecules in a hierarchical manner. The highest order classification of a molecule is Class. A molecule can be classified by any one of 4 classes: Mainly Alpha, Mainly Beta, Alpha Beta, and Few Secondary Structures <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>. Another level of classification which is on a lower order than class is Architecture. This level of classification is used to identify the shape of the domain structure using the orientation of secondary structures but ignoring the way they are connected to each other <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>. A third level of classification is Topology, which is also called Fold Group. This classification concerns the shared similarity of overall shape and connectivity of the secondary structures in the domain core <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>. The Homologous superfamily refers to a fourth classification type. This hierarchy groups together protein domains which are thought to share a common ancestor, according to specific criteria <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>.		Glutamine Synthetase (GS) has 2 prominent CATH domains. CATH is an acronym for Class (C), Architecture (A), Topology (T), and Homologous superfamily (H), which are categories for protein classification. Each of the aforementioned levels are used to classify molecules in a hierarchical manner. The highest order classification of a molecule is Class. A molecule can be classified by any one of 4 classes: Mainly Alpha, Mainly Beta, Alpha Beta, and Few Secondary Structures <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>. Another level of classification which is on a lower order than class is Architecture. This level of classification is used to identify the shape of the domain structure using the orientation of secondary structures but ignoring the way they are connected to each other <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>. A third level of classification is Topology, which is also called Fold Group. This classification concerns the shared similarity of overall shape and connectivity of the secondary structures in the domain core <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>. The Homologous superfamily refers to a fourth classification type. This hierarchy groups together protein domains which are thought to share a common ancestor, according to specific criteria <ref name="rasmol"> CATH Protein Structure Classification." CATH. 03 Sep 2008. Orengo group projects. 7 Dec 2008 http://www.cathdb.info/</ref>.

-	Looking at Glutamine Synthetase in ''Salmonella typhimurium'', we can identify 2 CATH domains. Each of the domains are of the class Alpha Beta, however, that is the only common aspect between the two. Alpha Beta includes both alternating alpha/beta structures and alpha+beta structures. <scene name='User:Steven_Tuyishime/Domain_from_104_to_456/1'>One domain begins at residue 104 and goes to residue 456</scene>. For this domain, the Architecture is a <scene name='User:Steven_Tuyishime/2_layer_sandwich/3'>2 layer sandwich</scene>. The Topology is Creatine Kinase; Chain A, domain 2 and the Homologous superfamily is Creatine Kinase; Chain. This domain is the larger of the two and has a COOH terminus.	+	Looking at Glutamine Synthetase in ''Salmonella typhimurium'', we can identify <scene name='User:Steven_Tuyishime/2_cath_domains/1'>2 CATH domains</scene>, with the smaller domain encompassing residues 1-103 (in red) and the other residues 104-456 (in blue). Each of the domains are of the class Alpha Beta, however, that is the only common aspect between the two. Alpha Beta includes both alternating alpha/beta structures and alpha+beta structures. <scene name='User:Steven_Tuyishime/Domain_from_104_to_456/1'>One domain begins at residue 104 and goes to residue 456</scene>. For this domain, the Architecture is a <scene name='User:Steven_Tuyishime/2_layer_sandwich/3'>2 layer sandwich</scene>. The Topology is Creatine Kinase; Chain A, domain 2 and the Homologous superfamily is Creatine Kinase; Chain. This domain is the larger of the two and has a COOH terminus.

	<scene name='User:Steven_Tuyishime/Domain_from_1_to_103/1'>		<scene name='User:Steven_Tuyishime/Domain_from_1_to_103/1'>